The
recently released CDC sequences
from H3N2v cases in Indiana and Ohio raises additional concerns of
human adaptation and an increase in transmission. All of the
Indiana and Ohio isolates match
the novel H3N2 sub-clade first reported in the West
Virginia cluster at a Mineral County day care center. The
sub-clade swapped out an N2 gene that has a lineage common in H1N2
swine and replaced it with a lineage found in H3N2 swine.

This novel sub-clade
raised initial concerns because the index case (A/West Virginia/06/2011)
and confirmed contact (A/West Virginia/07/2011)
had no swine exposure, and the disease onset dates signaled additional
transmission at the daycare center. Initial data from an
epidemiological studied identified ILI (influenza-like illness) in 23
of the 70 contacts of the index case, leading to a series of warnings
by the CDC in late 2011 and early 2012.

These warnings however
did not lead to any reported H3N2v during the peak of the 2011/2012 flu
season, once again highlighting surveillance issues regarding detection
of variants during the flu season. The first human H3N2v cases
identified in March 29, 2012 collection from a Utah case
(A/Utah/10/2012) confirming the onward spread of this sub-clade, which
was confirmed by sequences from July isolates from cases in Hawaii,
Indiana, and Ohio.

The initial sequences
from Indiana were from four cases at the LaPorte County fair. All
four sets of sequences (A/Indiana/06/2012, A/Indiana/07/2012,
A/Indiana/08/2012, A/Indiana/09/2012) were identical and included
a newly acquired N2 change, N234D (N2 numbering), which abolished the
glycosylation site. This change was not present in the earlier
human H3N2v cases, or the July Indiana sequence from the Jackson County
Fair, A/Indiana/12/2012. However, it was in the first July isolate from
Ohio, which was from the Butler County Fair, A/Ohio/13/2012.

The CDC release 10
additional sets of sequences from four cases in Indiana and 6 cases
from Ohio. All of the additional Ohio sequences were closely
related to the first sequence, suggesting all were from the Butler
County Fair and all had N234D. In contrast the four additional
cases from Indiana formed two additional distinct clusters. Two
(A/Indiana/13/2012, A/Indiana/17/2012) were similar but distinct from
the Jackson County sequence, while the other two were closely related
to each other (A/Indiana/15/2012 and A/Indiana/19/2012) but distinct
from the other Jackson County cluster. These patterns suggest
that the five Indiana isolates that are not from LaPorte are from
Jackson County and adjacent Jennings County. However, none of the
Indiana sequences which are distinct from the LaPorte sequence have
N234D.

The LaPorte cluster
included at least 5 confirmed cases, but the number of symptomatic
cases was markedly highly, signaling efficient human transmission at
the fair. Similarly, there were 14 confirmed cases linked to the
Butler County Fair, and the number of confirmed Butler County sequences
has increased to 17, which also signaled increased human transmission.

The finding of N234D in
all of the LaPorte County, Indiana (located in northwestern Indiana)
and Butler County, Ohio (located in southwestern Ohio) raises concerns
that this NA change is present in additional large clusters in Indiana
(Monroe and Washington Counties) as well as Ohio (Gallia and Champaign
Counties).

The loss of a
glycosylation site in the NA gene has parallels with the loss of a
glycosylation site in the HA gene in H5N1 transmission studies. N158D
was identified in transmission studies by Kawaoka, which used H5 clade
1 from Vietnam and Fouchier, which used clade 2.1 from Indonesia.
This loss of the glycosylation site was also seen in the Donis
transmission which used clade 2.2 from Egypt, which already had lost
the glycosylation site.

Thus, the loss of a
glycosylation site in the NA gene in two large H3N2v clusters in
Indiana and Ohio raise concerns that this change will be found in
additional clusters linked to the novel sub-clade that was first
identified in West Virginia in late 2011 and has been found in all
human H3N2v sequences from 2012.